We introduce PyHHMM, an object-oriented open-source Python implementation of Heterogeneous-Hidden Markov Models (HHMMs). In addition to HMM's basic core functionalities, such as different initialization algorithms and classical observations models, i.e., continuous and multinoulli, PyHHMM distinctively emphasizes features not supported in similar available frameworks: a heterogeneous observation model, missing data inference, different model order selection criterias, and semi-supervised training. These characteristics result in a feature-rich implementation for researchers working with sequential data. PyHHMM relies on the numpy, scipy, scikit-learn, and seaborn Python packages, and is distributed under the Apache-2.0 License. PyHHMM's source code is publicly available on Github (https://github.com/fmorenopino/HeterogeneousHMM) to facilitate adoptions and future contributions. A detailed documentation (https://pyhhmm.readthedocs.io/en/latest), which covers examples of use and models' theoretical explanation, is available. The package can be installed through the Python Package Index (PyPI), via 'pip install pyhhmm'.
Meta-learning (a.k.a. learning to learn) has recently emerged as a promising paradigm for a variety of applications. There are now many meta-learning methods, each focusing on different modeling aspects of base and meta learners, but all can be (re)formulated as specific bilevel optimization problems. This work presents BOML, a modularized optimization library that unifies several meta-learning algorithms into a common bilevel optimization framework. It provides a hierarchical optimization pipeline together with a variety of iteration modules, which can be used to solve the mainstream categori…
ParaMonte::Python (standing for Parallel Monte Carlo in Python) is a serial and MPI-parallelized library of (Markov Chain) Monte Carlo (MCMC) routines for sampling mathematical objective functions, in particular, the posterior distributions of parameters in Bayesian modeling and analysis in data science, Machine Learning, and scientific inference in general. In addition to providing access to fast high-performance serial/parallel Monte Carlo and MCMC sampling routines, the ParaMonte::Python library provides extensive post-processing and visualization tools that aim to automate and streamline t…
It is shown how the Python library Sympy can be used to compute symbolically the coefficients of the power series solution of the Lane-Emden equation (LEE). Sympy is an open source Python library for symbolic mathematics. The power series solutions are compared to the numerically computed solutions using matplotlib. The results of a run time measurement of the implemented algorithm are discussed at the end.
Petri Net is a formalism to describe changes between 2 or more states across discrete time and has been used to model many systems. We present PNet - a pure Python library for Petri Net modeling and simulation in Python programming language. The design of PNet focuses on reducing the learning curve needed to define a Petri Net by using a text-based language rather than programming constructs to define transition rules. Complex transition rules can be refined as regular Python functions. To demonstrate the simplicity of PNet, we present 2 examples - bread baking, and epidemiological models.
This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python bindings to access libcloudph++ from Fortran is presented.
Wrocław University of Science and Technology（弗罗茨瓦夫理工大学）；illimites foundation（伊利米特斯基金会）
scikit-multilearn is a Python library for performing multi-label classification. The library is compatible with the scikit/scipy ecosystem and uses sparse matrices for all internal operations. It provides native Python implementations of popular multi-label classification methods alongside a novel framework for label space partitioning and division. It includes modern algorithm adaptation methods, network-based label space division approaches, which extracts label dependency information and multi-label embedding classifiers. It provides python wrapped access to the extensive multi-label method…
PyArmadillo is a linear algebra library for the Python language, with the aim of closely mirroring the programming interface of the widely used Armadillo C++ library, which in turn is deliberately similar to Matlab. PyArmadillo hence facilitates algorithm prototyping with Matlab-like syntax directly in Python, and relatively straightforward conversion of PyArmadillo-based Python code into performant Armadillo-based C++ code. The converted code can be used for purposes such as speeding up Python-based programs in conjunction with pybind11, or the integration of algorithms originally prototyped …
The pyFAI package has been designed to reduce X-ray diffraction images into powder diffraction curves to be further processed by scientists. This contribution describes how to convert an image into a radial profile using the Numpy package, how the process was accelerated using Cython. The algorithm was parallelised, needing a complete re-design to benefit from massively parallel devices like graphical processing units or accelerators like the Intel Xeon Phi using the PyOpenCL library.
We present the Core Imaging Library (CIL), an open-source Python framework for tomographic imaging with particular emphasis on reconstruction of challenging datasets. Conventional filtered back-projection reconstruction tends to be insufficient for highly noisy, incomplete, non-standard or multi-channel data arising for example in dynamic, spectral and in situ tomography. CIL provides an extensive modular optimisation framework for prototyping reconstruction methods including sparsity and total variation regularisation, as well as tools for loading, preprocessing and visualising tomographic da…
Linear operators and optimisation are at the core of many algorithms used in signal and image processing, remote sensing, and inverse problems. For small to medium-scale problems, existing software packages (e.g., MATLAB, Python numpy and scipy) allow for explicitly building dense (or sparse) matrices and performing algebraic operations (e.g., computation of matrix-vector products and manipulation of matrices) with syntax that closely represents their corresponding analytical forms. However, many real application, large-scale operators do not lend themselves to explicit matrix representations,…
Bayesian Knowledge Tracing, a model used for cognitive mastery estimation, has been a hallmark of adaptive learning research and an integral component of deployed intelligent tutoring systems (ITS). In this paper, we provide a brief history of knowledge tracing model research and introduce pyBKT, an accessible and computationally efficient library of model extensions from the literature. The library provides data generation, fitting, prediction, and cross-validation routines, as well as a simple to use data helper interface to ingest typical tutor log dataset formats. We evaluate the runtime w…
We introduce giotto-ph, a high-performance, open-source software package for the computation of Vietoris-Rips barcodes. giotto-ph is based on Morozov and Nigmetov's lockfree (multicore) implementation of Ulrich Bauer's Ripser package. It also contains a re-working of the GUDHI library's implementation of Boissonnat and Pritam's Edge Collapser, which can be used as a pre-processing step to dramatically reduce overall run-times in certain scenarios. Our contribution is twofold: on the one hand, we integrate existing state-of-the-art ideas coherently in a single library and provide Python binding…
Raster Forge: Interactive Raster Manipulation Library and GUI for Python
COPELABS, Lusófona University（卢索福纳大学COPELABS实验室）；Center of Technology and Systems (UNINOVA-CTS)（技术与系统中心（UNINOVA-CTS））；Associated Lab of Intelligent Systems (LASI)（智能系统联合实验室）
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key findings published in journal articles, thereby making it difficult or impossible for the wider scientific community to verify the correctness of a result or to build further research on it. This paper presents a new Python-based library, PyRDM, whose functionality aims to automate the process of sharing the software and data via online, citable repositories …
